ingest exaspim spreadsheets

.gitignore

@@ -26,6 +26,12 @@ share/python-wheels/
 .installed.cfg
 *.egg
 MANIFEST
+scripts/MRI_ingest
+scripts/Exaspim_ingest/original_spec_files
+scripts/Exaspim_ingest/ExM Sample Tracking.xlsx
+scripts/Exaspim_ingest/output
+scripts/Exaspim_ingest/original_plus_materials
+scripts/Exaspim_ingest/tars_info
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -137,3 +143,6 @@ dmypy.json
 
 # MacOs
 **/.DS_Store
+
+# MRI stuff
+scripts/MRI_ingest/MRI_files/*

scripts/Exaspim_ingest/original_plus_materials/576404_procedures.json

@@ -0,0 +1,31 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
+   "schema_version": "0.13.3",
+   "subject_id": "576404",
+   "subject_procedures": [
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2021-07-12",
+         "experimenter_full_name": "28908",
+         "iacuc_protocol": "1806",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "procedure_type": "Perfusion",
+               "output_specimen_ids": [
+                  "576404"
+               ],
+               "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66"
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      }
+   ],
+   "specimen_procedures": [],
+   "notes": null
+}

scripts/Exaspim_ingest/original_plus_materials/603033_procedures.json

@@ -0,0 +1,31 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
+   "schema_version": "0.13.3",
+   "subject_id": "603033",
+   "subject_procedures": [
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2021-11-19",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "procedure_type": "Perfusion",
+               "output_specimen_ids": [
+                  "603033"
+               ],
+               "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66"
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      }
+   ],
+   "specimen_procedures": [],
+   "notes": null
+}

scripts/Exaspim_ingest/original_plus_materials/609105_procedures.json

@@ -0,0 +1,67 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
+   "schema_version": "0.13.3",
+   "subject_id": "609105",
+   "subject_procedures": [
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2021-12-09",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "recovery_time": null,
+               "recovery_time_unit": "minute",
+               "injection_duration": null,
+               "injection_duration_unit": "minute",
+               "instrument_id": null,
+               "procedure_type": "Retro-orbital injection",
+               "injection_volume": null,
+               "injection_volume_unit": "microliter",
+               "injection_eye": null,
+               "injection_materials": [
+                  {
+                     "material_type": "Virus",
+                     "name": "AAV-PHP-eB_Syn-Flex TRE-2tTA",
+                     "tars_identifiers": null,
+                     "addgene_id": null,
+                     "titer": 30000000000,
+                     "titer_unit": "gc/mL"
+                  }
+               ]
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      },
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2022-01-06",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "procedure_type": "Perfusion",
+               "output_specimen_ids": [
+                  "609105"
+               ],
+               "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66"
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      }
+   ],
+   "specimen_procedures": [],
+   "notes": null
+}

scripts/Exaspim_ingest/original_plus_materials/609107_procedures.json

@@ -0,0 +1,67 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
+   "schema_version": "0.13.3",
+   "subject_id": "609107",
+   "subject_procedures": [
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2021-12-09",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "recovery_time": null,
+               "recovery_time_unit": "minute",
+               "injection_duration": null,
+               "injection_duration_unit": "minute",
+               "instrument_id": null,
+               "procedure_type": "Retro-orbital injection",
+               "injection_volume": null,
+               "injection_volume_unit": "microliter",
+               "injection_eye": null,
+               "injection_materials": [
+                  {
+                     "material_type": "Virus",
+                     "name": "AAV-PHP-eB_Syn-Flex TRE-2tTA",
+                     "tars_identifiers": null,
+                     "addgene_id": null,
+                     "titer": 30000000000,
+                     "titer_unit": "gc/mL"
+                  }
+               ]
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      },
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2022-01-06",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "procedure_type": "Perfusion",
+               "output_specimen_ids": [
+                  "609107"
+               ],
+               "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66"
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      }
+   ],
+   "specimen_procedures": [],
+   "notes": null
+}

scripts/Exaspim_ingest/original_plus_materials/609281_procedures.json

@@ -0,0 +1,67 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
+   "schema_version": "0.13.3",
+   "subject_id": "609281",
+   "subject_procedures": [
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2021-12-09",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "recovery_time": null,
+               "recovery_time_unit": "minute",
+               "injection_duration": null,
+               "injection_duration_unit": "minute",
+               "instrument_id": null,
+               "procedure_type": "Retro-orbital injection",
+               "injection_volume": null,
+               "injection_volume_unit": "microliter",
+               "injection_eye": null,
+               "injection_materials": [
+                  {
+                     "material_type": "Virus",
+                     "name": "AAV-PHP-eB_Syn-Flex TRE-2tTA",
+                     "tars_identifiers": null,
+                     "addgene_id": null,
+                     "titer": 30000000000,
+                     "titer_unit": "gc/mL"
+                  }
+               ]
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      },
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2022-01-05",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2107",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "procedure_type": "Perfusion",
+               "output_specimen_ids": [
+                  "609281"
+               ],
+               "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66"
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      }
+   ],
+   "specimen_procedures": [],
+   "notes": null
+}

scripts/Exaspim_ingest/original_plus_materials/613814_procedures.json

@@ -0,0 +1,67 @@
+{
+   "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/procedures.py",
+   "schema_version": "0.13.3",
+   "subject_id": "613814",
+   "subject_procedures": [
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2022-01-11",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2109",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "recovery_time": null,
+               "recovery_time_unit": "minute",
+               "injection_duration": null,
+               "injection_duration_unit": "minute",
+               "instrument_id": null,
+               "procedure_type": "Retro-orbital injection",
+               "injection_volume": null,
+               "injection_volume_unit": "microliter",
+               "injection_eye": null,
+               "injection_materials": [
+                  {
+                     "material_type": "Virus",
+                     "name": "AAV-PHP-eB_Syn-Flex TRE-2tTA",
+                     "tars_identifiers": null,
+                     "addgene_id": null,
+                     "titer": 30000000000,
+                     "titer_unit": "gc/mL"
+                  }
+               ]
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      },
+      {
+         "procedure_type": "Surgery",
+         "start_date": "2022-02-07",
+         "experimenter_full_name": "13040",
+         "iacuc_protocol": "2109",
+         "animal_weight_prior": null,
+         "animal_weight_post": null,
+         "weight_unit": "gram",
+         "anaesthesia": null,
+         "workstation_id": null,
+         "procedures": [
+            {
+               "procedure_type": "Perfusion",
+               "output_specimen_ids": [
+                  "613814"
+               ],
+               "protocol_id": "dx.doi.org/10.17504/protocols.io.bg5vjy66"
+            }
+         ],
+         "notes": null,
+         "protocol_id": "dx.doi.org/10.17504/protocols.io.kqdg392o7g25/v1"
+      }
+   ],
+   "specimen_procedures": [],
+   "notes": null
+}